Casal2 Test Case MPD comparisons for BCO

1 BCO comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-7 vs. 2e-5).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-7 vs. 2e-5).

1.1 BCO model characteristics

The main characteristics of the Test Case BCO (ling) CASAL model are:

• one stock, ages 3 - 20
• one area
• years 1900 - 2019, projection year 2020
• one time step
• two stock categories: male and female
• natural mortality-at-age is 0.14 for males and 0.20 for females
• sex-specific logistic maturity
• sex-specific von Bertalanffy age-length relationship
• one length-weight relationship (\(W = aL^b\))
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.75 and \(\sigma_R\) 0.6
• no ageing error
• one survey with sex-specific age-based logistic selectivity
• three fisheries, all with sex-specific length-based logistic selectivity and retained/discarded catches

Observation data include:

• survey index
• fishery CPUE index
• fishery proportions-at-length

Parameters estimated include:

• B0
• male \(L_{\infty}\)
• male age-length CV2
• sex-specific survey logistic selectivity (a50 and ato95)
• YCS (recruitment deviations)

1.2 R environment

## [1] "Mon Sep 27 19:59:50 2021"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 11 (bullseye)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_21.08   casal_2.30     devtools_2.4.2 usethis_2.0.1  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.5 
## [11] tidyr_1.1.3    huxtable_5.4.0 dplyr_1.0.7    plyr_1.8.6    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7         lattice_0.20-41    prettyunits_1.1.1  ps_1.6.0          
##  [5] assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.27      utf8_1.2.2        
##  [9] R6_2.5.1           evaluate_0.14      pillar_1.6.2       rlang_0.4.11      
## [13] rstudioapi_0.13    data.table_1.14.0  callr_3.7.0        jquerylib_0.1.4   
## [17] rmarkdown_2.11     desc_1.3.0         stringr_1.4.0      munsell_0.5.0     
## [21] compiler_3.6.3     xfun_0.26          pkgconfig_2.0.3    pkgbuild_1.2.0    
## [25] htmltools_0.5.2    tidyselect_1.1.1   tibble_3.1.4       reshape_0.8.8     
## [29] fansi_0.5.0        crayon_1.4.1       withr_2.4.2        grid_3.6.3        
## [33] jsonlite_1.7.2     GGally_2.1.2       gtable_0.3.0       lifecycle_1.0.0   
## [37] DBI_1.1.1          magrittr_2.0.1     scales_1.1.1       cli_3.0.1         
## [41] stringi_1.7.4      cachem_1.0.6       remotes_2.4.0      fs_1.5.0          
## [45] testthat_3.0.4     bslib_0.3.0        ellipsis_0.3.2     generics_0.1.0    
## [49] vctrs_0.3.8        RColorBrewer_1.1-2 tools_3.6.3        glue_1.4.2        
## [53] purrr_0.3.4        processx_3.5.2     pkgload_1.2.2      fastmap_1.1.0     
## [57] yaml_2.2.1         colorspace_2.0-2   sessioninfo_1.1.1  memoise_2.0.0     
## [61] knitr_1.34         sass_0.4.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
initialization.B0	14170.00000	14170.00000	0.000
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	1.00000	1.00000	0.000
recruitment.YCS6	1.00000	1.00000	0.000
recruitment.YCS7	1.00000	1.00000	0.000
recruitment.YCS8	1.00000	1.00000	0.000
recruitment.YCS9	1.00000	1.00000	0.000
recruitment.YCS10	1.00000	1.00000	0.000
recruitment.YCS11	1.00000	1.00000	0.000
recruitment.YCS12	1.00000	1.00000	0.000
recruitment.YCS13	1.00000	1.00000	0.000
recruitment.YCS14	1.00000	1.00000	0.000
recruitment.YCS15	1.00000	1.00000	0.000
recruitment.YCS16	1.00000	1.00000	0.000
recruitment.YCS17	1.00000	1.00000	0.000
recruitment.YCS18	1.00000	1.00000	0.000
recruitment.YCS19	1.00000	1.00000	0.000
recruitment.YCS20	1.00000	1.00000	0.000
recruitment.YCS21	1.00000	1.00000	0.000
recruitment.YCS22	1.00000	1.00000	0.000
recruitment.YCS23	1.00000	1.00000	0.000
recruitment.YCS24	1.00000	1.00000	0.000
recruitment.YCS25	1.00000	1.00000	0.000
recruitment.YCS26	1.00000	1.00000	0.000
recruitment.YCS27	1.00000	1.00000	0.000
recruitment.YCS28	1.00000	1.00000	0.000
recruitment.YCS29	1.00000	1.00000	0.000
recruitment.YCS30	1.00000	1.00000	0.000
recruitment.YCS31	1.00000	1.00000	0.000
recruitment.YCS32	1.00000	1.00000	0.000
recruitment.YCS33	1.00000	1.00000	0.000
recruitment.YCS34	1.00000	1.00000	0.000
recruitment.YCS35	1.00000	1.00000	0.000
recruitment.YCS36	1.00000	1.00000	0.000
recruitment.YCS37	1.00000	1.00000	0.000
recruitment.YCS38	1.00000	1.00000	0.000
recruitment.YCS39	1.00000	1.00000	0.000
recruitment.YCS40	1.00000	1.00000	0.000
recruitment.YCS41	1.00000	1.00000	0.000
recruitment.YCS42	1.00000	1.00000	0.000
recruitment.YCS43	1.00000	1.00000	0.000
recruitment.YCS44	1.00000	1.00000	0.000
recruitment.YCS45	1.00000	1.00000	0.000
recruitment.YCS46	1.00000	1.00000	0.000
recruitment.YCS47	1.00000	1.00000	0.000
recruitment.YCS48	1.00000	1.00000	0.000
recruitment.YCS49	1.00000	1.00000	0.000
recruitment.YCS50	1.00000	1.00000	0.000
recruitment.YCS51	1.00000	1.00000	0.000
recruitment.YCS52	1.00000	1.00000	0.000
recruitment.YCS53	1.00000	1.00000	0.000
recruitment.YCS54	1.00000	1.00000	0.000
recruitment.YCS55	1.00000	1.00000	0.000
recruitment.YCS56	1.00000	1.00000	0.000
recruitment.YCS57	1.00000	1.00000	0.000
recruitment.YCS58	1.00000	1.00000	0.000
recruitment.YCS59	1.00000	1.00000	0.000
recruitment.YCS60	1.00000	1.00000	0.000
recruitment.YCS61	1.00000	1.00000	0.000
recruitment.YCS62	1.00000	1.00000	0.000
recruitment.YCS63	1.00000	1.00000	0.000
recruitment.YCS64	1.00000	1.00000	0.000
recruitment.YCS65	1.00000	1.00000	0.000
recruitment.YCS66	1.00000	1.00000	0.000
recruitment.YCS67	1.00000	1.00000	0.000
recruitment.YCS68	1.00000	1.00000	0.000
recruitment.YCS69	1.00000	1.00000	0.000
recruitment.YCS70	1.00000	1.00000	0.000
recruitment.YCS71	1.00000	1.00000	0.000
recruitment.YCS72	1.00000	1.00000	0.000
recruitment.YCS73	1.00000	1.00000	0.000
recruitment.YCS74	1.00000	1.00000	0.000
recruitment.YCS75	1.00000	1.00000	0.000
recruitment.YCS76	1.00000	1.00000	0.000
recruitment.YCS77	1.00000	1.00000	0.000
recruitment.YCS78	1.00000	1.00000	0.000
recruitment.YCS79	1.00000	1.00000	0.000
recruitment.YCS80	1.00000	1.00000	0.000
recruitment.YCS81	1.00000	1.00000	0.000
recruitment.YCS82	1.00000	1.00000	0.000
recruitment.YCS83	1.00000	1.00000	0.000
recruitment.YCS84	0.23480	0.23480	0.000
recruitment.YCS85	0.23160	0.23160	0.000
recruitment.YCS86	0.23220	0.23220	0.000
recruitment.YCS87	0.24120	0.24120	0.000
recruitment.YCS88	0.26510	0.26510	0.000
recruitment.YCS89	0.31720	0.31720	0.000
recruitment.YCS90	0.42240	0.42240	0.000
recruitment.YCS91	0.61390	0.61390	0.000
recruitment.YCS92	0.92300	0.92300	0.000
recruitment.YCS93	1.42900	1.42900	0.000
recruitment.YCS94	1.48000	1.48000	0.000
recruitment.YCS95	1.00900	1.00900	0.000
recruitment.YCS96	0.84620	0.84620	0.000
recruitment.YCS97	0.85550	0.85550	0.000
recruitment.YCS98	1.08700	1.08700	0.000
recruitment.YCS99	1.53000	1.53000	0.000
recruitment.YCS100	1.02700	1.02700	0.000
recruitment.YCS101	0.79990	0.79990	0.000
recruitment.YCS102	0.82080	0.82080	0.000
recruitment.YCS103	0.63180	0.63180	0.000
recruitment.YCS104	0.80520	0.80520	0.000
recruitment.YCS105	0.74530	0.74530	0.000
recruitment.YCS106	0.46340	0.46340	0.000
recruitment.YCS107	1.07500	1.07500	0.000
recruitment.YCS108	0.89920	0.89920	0.000
recruitment.YCS109	0.38510	0.38510	0.000
recruitment.YCS110	0.91270	0.91270	0.000
recruitment.YCS111	0.70920	0.70920	0.000
recruitment.YCS112	0.82900	0.82900	0.000
recruitment.YCS113	0.42330	0.42330	0.000
recruitment.YCS114	1.27800	1.27800	0.000
recruitment.YCS115	0.68810	0.68810	0.000
recruitment.YCS116	0.74250	0.74250	0.000
recruitment.YCS117	0.57050	0.57050	0.000
recruitment.YCS118	0.45160	0.45160	0.000
recruitment.YCS119	1.00000	1.00000	0.000
recruitment.YCS120	1.00000	1.00000	0.000
size_at_age.Linf_male	47.12000	47.12000	0.000
size_at_age.cv2_male	0.06256	0.06256	0.000
selectivity[potSsel].male1	3.03900	3.03900	0.000
selectivity[potSsel].male2	0.19070	0.19060	0.052
selectivity[potSsel].female1	3.31600	3.31600	0.000
selectivity[potSsel].female2	1.04500	1.04500	0.000

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	13871.00000	13879.10000	13871.00000	13871.10000	13879.10000	13871.00000
age_length[asMm0].linf	46.66120	46.65740	46.66130	46.66130	46.65730	46.66130
age_length[asMm0].cv_last	0.02027	0.02260	0.02027	0.02028	0.02260	0.02027
selectivity[potSurveySel_male].a50	3.04313	3.03927	3.03852	3.02547	3.04823	3.02520
selectivity[potSurveySel_male].ato95	0.21319	0.19134	0.19039	0.12587	0.23497	0.12457
selectivity[potSurveySel_female].a50	3.32403	3.32488	3.32403	3.32402	3.32489	3.32403
selectivity[potSurveySel_female].ato95	1.07886	1.07224	1.07887	1.07887	1.07225	1.07887
process[Recruitment].ycs_values{1980}	0.21202	0.21193	0.21202	0.21199	0.21190	0.21202
process[Recruitment].ycs_values{1981}	0.20885	0.20878	0.20885	0.20876	0.20877	0.20885
process[Recruitment].ycs_values{1982}	0.20941	0.20939	0.20941	0.20954	0.20942	0.20941
process[Recruitment].ycs_values{1983}	0.21760	0.21762	0.21760	0.21760	0.21763	0.21760
process[Recruitment].ycs_values{1984}	0.24042	0.24046	0.24042	0.24042	0.24046	0.24042
process[Recruitment].ycs_values{1985}	0.29290	0.29290	0.29291	0.29291	0.29290	0.29291
process[Recruitment].ycs_values{1986}	0.40043	0.40029	0.40043	0.40043	0.40029	0.40043
process[Recruitment].ycs_values{1987}	0.60038	0.60005	0.60039	0.60038	0.60004	0.60039
process[Recruitment].ycs_values{1988}	0.92667	0.92623	0.92661	0.92660	0.92631	0.92661
process[Recruitment].ycs_values{1989}	1.47526	1.47532	1.47521	1.47522	1.47513	1.47521
process[Recruitment].ycs_values{1990}	1.59614	1.59697	1.59625	1.59625	1.59718	1.59625
process[Recruitment].ycs_values{1991}	1.00472	1.00531	1.00468	1.00470	1.00525	1.00468
process[Recruitment].ycs_values{1992}	0.83552	0.83594	0.83556	0.83556	0.83594	0.83556
process[Recruitment].ycs_values{1993}	0.85248	0.85251	0.85251	0.85250	0.85251	0.85251
process[Recruitment].ycs_values{1994}	1.11068	1.10949	1.11052	1.11053	1.10945	1.11052
process[Recruitment].ycs_values{1995}	1.66456	1.66318	1.66458	1.66456	1.66332	1.66458
process[Recruitment].ycs_values{1996}	1.05327	1.05404	1.05334	1.05336	1.05395	1.05334
process[Recruitment].ycs_values{1997}	0.82392	0.82398	0.82395	0.82394	0.82399	0.82395
process[Recruitment].ycs_values{1998}	0.84394	0.84390	0.84390	0.84389	0.84391	0.84390
process[Recruitment].ycs_values{1999}	0.62169	0.62189	0.62168	0.62168	0.62189	0.62168
process[Recruitment].ycs_values{2000}	0.74184	0.74236	0.74184	0.74184	0.74236	0.74184
process[Recruitment].ycs_values{2001}	0.67333	0.67356	0.67333	0.67333	0.67356	0.67333
process[Recruitment].ycs_values{2002}	0.44396	0.44396	0.44396	0.44396	0.44396	0.44396
process[Recruitment].ycs_values{2003}	1.21010	1.20740	1.21010	1.21009	1.20740	1.21010
process[Recruitment].ycs_values{2004}	1.22006	1.21557	1.22005	1.22005	1.21557	1.22005
process[Recruitment].ycs_values{2005}	0.48932	0.48725	0.48932	0.48932	0.48725	0.48932
process[Recruitment].ycs_values{2006}	1.00364	1.00000	1.00363	1.00363	1.00000	1.00363
process[Recruitment].ycs_values{2007}	0.71187	0.72299	0.71187	0.71187	0.72300	0.71187
process[Recruitment].ycs_values{2008}	0.83132	0.83048	0.83132	0.83132	0.83048	0.83132
process[Recruitment].ycs_values{2009}	0.42153	0.42128	0.42153	0.42153	0.42128	0.42153
process[Recruitment].ycs_values{2010}	1.26131	1.26096	1.26131	1.26131	1.26096	1.26131
process[Recruitment].ycs_values{2011}	0.66527	0.66603	0.66527	0.66527	0.66603	0.66527
process[Recruitment].ycs_values{2012}	0.70938	0.70952	0.70938	0.70938	0.70952	0.70938
process[Recruitment].ycs_values{2013}	0.55184	0.55165	0.55184	0.55184	0.55165	0.55184
process[Recruitment].ycs_values{2014}	0.42967	0.42938	0.42967	0.42967	0.42938	0.42967

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	-0.058	0.000	-0.001	-0.058	0.000
age_length[asMm0].linf	0.000	0.008	-0.000	-0.000	0.008	-0.000
age_length[asMm0].cv_last	0.000	-11.507	-0.001	-0.079	-11.481	-0.001
selectivity[potSurveySel_male].a50	0.000	0.127	0.151	0.580	-0.168	0.589
selectivity[potSurveySel_male].ato95	0.000	10.249	10.698	40.957	-10.214	41.569
selectivity[potSurveySel_female].a50	0.000	-0.026	0.000	0.000	-0.026	0.000
selectivity[potSurveySel_female].ato95	0.000	0.614	-0.001	-0.001	0.613	-0.001
process[Recruitment].ycs_values{1980}	0.000	0.040	0.000	0.012	0.054	0.000
process[Recruitment].ycs_values{1981}	0.000	0.033	0.000	0.044	0.037	0.000
process[Recruitment].ycs_values{1982}	0.000	0.012	0.000	-0.058	-0.002	0.000
process[Recruitment].ycs_values{1983}	0.000	-0.010	0.000	-0.000	-0.012	0.000
process[Recruitment].ycs_values{1984}	0.000	-0.016	-0.000	-0.000	-0.016	-0.000
process[Recruitment].ycs_values{1985}	0.000	0.002	-0.001	-0.001	0.002	-0.001
process[Recruitment].ycs_values{1986}	0.000	0.034	-0.000	0.000	0.034	-0.000
process[Recruitment].ycs_values{1987}	0.000	0.054	-0.002	-0.001	0.055	-0.002
process[Recruitment].ycs_values{1988}	0.000	0.048	0.006	0.007	0.039	0.006
process[Recruitment].ycs_values{1989}	0.000	-0.004	0.003	0.003	0.009	0.003
process[Recruitment].ycs_values{1990}	0.000	-0.052	-0.007	-0.007	-0.065	-0.007
process[Recruitment].ycs_values{1991}	0.000	-0.059	0.004	0.002	-0.053	0.004
process[Recruitment].ycs_values{1992}	0.000	-0.051	-0.005	-0.005	-0.051	-0.005
process[Recruitment].ycs_values{1993}	0.000	-0.004	-0.003	-0.003	-0.004	-0.003
process[Recruitment].ycs_values{1994}	0.000	0.107	0.014	0.014	0.111	0.014
process[Recruitment].ycs_values{1995}	0.000	0.083	-0.001	0.000	0.074	-0.001
process[Recruitment].ycs_values{1996}	0.000	-0.073	-0.007	-0.009	-0.065	-0.007
process[Recruitment].ycs_values{1997}	0.000	-0.008	-0.004	-0.003	-0.009	-0.004
process[Recruitment].ycs_values{1998}	0.000	0.004	0.004	0.005	0.003	0.004
process[Recruitment].ycs_values{1999}	0.000	-0.032	0.001	0.001	-0.033	0.001
process[Recruitment].ycs_values{2000}	0.000	-0.071	0.000	-0.000	-0.071	0.000
process[Recruitment].ycs_values{2001}	0.000	-0.034	0.001	0.000	-0.034	0.001
process[Recruitment].ycs_values{2002}	0.000	0.001	0.000	0.000	0.001	0.000
process[Recruitment].ycs_values{2003}	0.000	0.223	0.000	0.001	0.223	0.000
process[Recruitment].ycs_values{2004}	0.000	0.368	0.001	0.001	0.368	0.001
process[Recruitment].ycs_values{2005}	0.000	0.421	0.000	0.000	0.421	0.000
process[Recruitment].ycs_values{2006}	0.000	0.363	0.001	0.001	0.363	0.001
process[Recruitment].ycs_values{2007}	0.000	-1.563	0.000	0.000	-1.563	0.000
process[Recruitment].ycs_values{2008}	0.000	0.101	0.000	0.000	0.101	0.000
process[Recruitment].ycs_values{2009}	0.000	0.059	0.000	0.000	0.059	0.000
process[Recruitment].ycs_values{2010}	0.000	0.028	0.000	0.000	0.028	0.000
process[Recruitment].ycs_values{2011}	0.000	-0.114	0.000	-0.000	-0.114	0.000
process[Recruitment].ycs_values{2012}	0.000	-0.019	0.000	-0.000	-0.019	0.000
process[Recruitment].ycs_values{2013}	0.000	0.035	0.000	0.000	0.034	0.000
process[Recruitment].ycs_values{2014}	0.000	0.067	0.000	-0.000	0.067	0.000

CASAL objective function component values

Component	Base_Model	Sensitivity_1
potCPUE	-51.180	-51.180
potSurveyAbd	-3.254	-3.254
logbookLF	54.660	54.660
potCommAF	54.410	54.410
potSurveyAF	118.200	118.200
recCatchLF	68.040	68.040
prior_on_initialization.B0	9.559	9.559
prior_on_recruitment.YCS	9.658	9.658
prior_on_size_at_age.Linf_male	0.000	0.000
prior_on_size_at_age.cv2_male	0.000	0.000
prior_on_selectivity[potSsel].male	0.000	0.000
prior_on_selectivity[potSsel].female	0.000	0.000
prior_on_q_qPotCPUE	-8.331	-8.331
prior_on_q_potSurveyq	-11.380	-11.380
clp1F	0.000	0.000
clp2F	0.000	0.000
clp3F	0.000	0.000
YCS	0.566	0.566
Total	241.000	241.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->potSurvey-2010	-0.789	-0.793	-0.789	-0.789	-0.793	-0.789
observation->potSurvey-2014	-0.931	-0.933	-0.931	-0.931	-0.933	-0.931
observation->potSurvey-2018	-1.120	-1.121	-1.120	-1.120	-1.121	-1.120
observation->potCPUE-1990	1.126	1.129	1.126	1.125	1.129	1.126
observation->potCPUE-1991	2.227	2.233	2.227	2.227	2.233	2.227
observation->potCPUE-1992	-0.686	-0.682	-0.686	-0.686	-0.682	-0.686
observation->potCPUE-1993	-1.938	-1.937	-1.938	-1.938	-1.937	-1.938
observation->potCPUE-1994	-2.140	-2.140	-2.140	-2.140	-2.140	-2.140
observation->potCPUE-1995	-2.056	-2.056	-2.056	-2.056	-2.056	-2.056
observation->potCPUE-1996	-2.194	-2.194	-2.194	-2.194	-2.194	-2.194
observation->potCPUE-1997	-2.026	-2.025	-2.026	-2.026	-2.025	-2.026
observation->potCPUE-1998	-2.164	-2.165	-2.164	-2.164	-2.165	-2.164
observation->potCPUE-1999	-1.736	-1.734	-1.736	-1.736	-1.734	-1.736
observation->potCPUE-2000	-2.194	-2.194	-2.194	-2.194	-2.194	-2.194
observation->potCPUE-2001	-2.173	-2.173	-2.173	-2.173	-2.173	-2.173
observation->potCPUE-2002	-2.084	-2.084	-2.084	-2.084	-2.084	-2.084
observation->potCPUE-2003	-2.187	-2.187	-2.187	-2.187	-2.187	-2.187
observation->potCPUE-2004	-2.185	-2.185	-2.185	-2.185	-2.185	-2.185
observation->potCPUE-2005	-1.894	-1.895	-1.894	-1.894	-1.895	-1.894
observation->potCPUE-2006	-1.596	-1.601	-1.596	-1.596	-1.601	-1.596
observation->potCPUE-2007	-1.999	-2.003	-1.999	-1.999	-2.003	-1.999
observation->potCPUE-2008	-1.932	-1.936	-1.932	-1.932	-1.936	-1.932
observation->potCPUE-2009	-1.631	-1.633	-1.631	-1.631	-1.633	-1.631
observation->potCPUE-2010	-2.186	-2.186	-2.186	-2.186	-2.186	-2.186
observation->potCPUE-2011	-1.876	-1.866	-1.876	-1.876	-1.866	-1.876
observation->potCPUE-2012	-1.908	-1.898	-1.908	-1.908	-1.898	-1.908
observation->potCPUE-2013	-1.959	-1.955	-1.959	-1.959	-1.955	-1.959
observation->potCPUE-2014	-1.313	-1.311	-1.313	-1.313	-1.311	-1.313
observation->potCPUE-2015	-1.908	-1.909	-1.908	-1.908	-1.909	-1.908
observation->potCPUE-2016	-2.082	-2.083	-2.082	-2.082	-2.083	-2.082
observation->potCPUE-2017	-2.037	-2.039	-2.037	-2.037	-2.039	-2.037
observation->potCPUE-2018	-1.654	-1.650	-1.654	-1.654	-1.650	-1.654
observation->AFpotSurvey-2010	35.036	35.085	35.036	35.036	35.085	35.036
observation->AFpotSurvey-2014	38.718	38.720	38.718	38.718	38.720	38.718
observation->AFpotSurvey-2018	38.821	38.791	38.821	38.821	38.791	38.821
observation->AFpotFishing-2018	45.611	45.653	45.611	45.611	45.653	45.611
observation->AFpotFishing-2019	7.854	7.854	7.854	7.854	7.854	7.854
observation->lgobookLF	51.538	51.541	51.538	51.537	51.541	51.538
observation->rec.catch.LF	71.222	72.113	71.222	71.222	72.113	71.222
prior->B0->process[Recruitment].b0	9.538	9.538	9.538	9.538	9.538	9.538
prior->male_Linf->age_length[asMm0].linf	0.000	0.000	0.000	0.000	0.000	0.000
prior->male_cv2->age_length[asMm0].cv_last	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mA50->selectivity[potSurveySel_male].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_mAto95->selectivity[potSurveySel_male].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fA50->selectivity[potSurveySel_female].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->potSurvey_fAto95->selectivity[potSurveySel_female].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->YCS->process[Recruitment].ycs_values{1980}	1.624	1.625	1.624	1.624	1.626	1.624
prior->YCS->process[Recruitment].ycs_values{1981}	1.678	1.679	1.678	1.679	1.679	1.678
prior->YCS->process[Recruitment].ycs_values{1982}	1.668	1.668	1.668	1.666	1.668	1.668
prior->YCS->process[Recruitment].ycs_values{1983}	1.533	1.533	1.533	1.533	1.533	1.533
prior->YCS->process[Recruitment].ycs_values{1984}	1.204	1.204	1.204	1.204	1.204	1.204
prior->YCS->process[Recruitment].ycs_values{1985}	0.648	0.648	0.648	0.648	0.648	0.648
prior->YCS->process[Recruitment].ycs_values{1986}	0.028	0.028	0.028	0.028	0.028	0.028
prior->YCS->process[Recruitment].ycs_values{1987}	-0.304	-0.303	-0.304	-0.304	-0.303	-0.304
prior->YCS->process[Recruitment].ycs_values{1988}	-0.066	-0.067	-0.066	-0.066	-0.067	-0.066
prior->YCS->process[Recruitment].ycs_values{1989}	0.868	0.868	0.867	0.867	0.867	0.867
prior->YCS->process[Recruitment].ycs_values{1990}	1.095	1.097	1.096	1.096	1.097	1.096
prior->YCS->process[Recruitment].ycs_values{1991}	0.046	0.046	0.045	0.046	0.046	0.045
prior->YCS->process[Recruitment].ycs_values{1992}	-0.179	-0.178	-0.179	-0.179	-0.178	-0.179
prior->YCS->process[Recruitment].ycs_values{1993}	-0.160	-0.160	-0.160	-0.160	-0.160	-0.160
prior->YCS->process[Recruitment].ycs_values{1994}	0.214	0.212	0.214	0.214	0.212	0.214
prior->YCS->process[Recruitment].ycs_values{1995}	1.225	1.222	1.225	1.225	1.223	1.225
prior->YCS->process[Recruitment].ycs_values{1996}	0.121	0.122	0.121	0.121	0.122	0.121
prior->YCS->process[Recruitment].ycs_values{1997}	-0.191	-0.191	-0.191	-0.191	-0.191	-0.191
prior->YCS->process[Recruitment].ycs_values{1998}	-0.169	-0.169	-0.169	-0.169	-0.169	-0.169
prior->YCS->process[Recruitment].ycs_values{1999}	-0.307	-0.307	-0.307	-0.307	-0.307	-0.307
prior->YCS->process[Recruitment].ycs_values{2000}	-0.264	-0.264	-0.264	-0.264	-0.264	-0.264
prior->YCS->process[Recruitment].ycs_values{2001}	-0.300	-0.300	-0.300	-0.300	-0.300	-0.300
prior->YCS->process[Recruitment].ycs_values{2002}	-0.107	-0.107	-0.107	-0.107	-0.107	-0.107
prior->YCS->process[Recruitment].ycs_values{2003}	0.384	0.379	0.384	0.384	0.379	0.384
prior->YCS->process[Recruitment].ycs_values{2004}	0.401	0.393	0.401	0.401	0.393	0.401
prior->YCS->process[Recruitment].ycs_values{2005}	-0.203	-0.199	-0.203	-0.203	-0.199	-0.203
prior->YCS->process[Recruitment].ycs_values{2006}	0.044	0.038	0.044	0.044	0.038	0.044
prior->YCS->process[Recruitment].ycs_values{2007}	-0.284	-0.277	-0.284	-0.284	-0.277	-0.284
prior->YCS->process[Recruitment].ycs_values{2008}	-0.183	-0.184	-0.183	-0.183	-0.184	-0.183
prior->YCS->process[Recruitment].ycs_values{2009}	-0.044	-0.043	-0.044	-0.044	-0.043	-0.044
prior->YCS->process[Recruitment].ycs_values{2010}	0.474	0.474	0.474	0.474	0.474	0.474
prior->YCS->process[Recruitment].ycs_values{2011}	-0.303	-0.303	-0.303	-0.303	-0.303	-0.303
prior->YCS->process[Recruitment].ycs_values{2012}	-0.285	-0.285	-0.285	-0.285	-0.285	-0.285
prior->YCS->process[Recruitment].ycs_values{2013}	-0.279	-0.278	-0.279	-0.279	-0.278	-0.279
prior->YCS->process[Recruitment].ycs_values{2014}	-0.068	-0.067	-0.068	-0.068	-0.067	-0.068
additional_prior->PrSurveyQ	-11.153	-11.154	-11.153	-11.153	-11.154	-11.153
additional_prior->PrCPUEQ	-8.207	-8.208	-8.207	-8.207	-8.208	-8.207
additional_prior->YCS_average_1	0.495	0.496	0.495	0.495	0.496	0.495
total_negloglike	237.802	238.776	237.802	237.802	238.776	237.802
total_score	237.802	238.776	237.802	237.802	238.776	237.802

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-005"                                                                 
## [2] "fmm: have converged: t = 1.53773e-005 f = 240.986"                                                       
## [3] "Successful convergence in optimise"                                                                      
## [4] "Minimiser achieved convergence after 91 quasi-Newton iterations using 101 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-007"                                                                                 
## [2] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [3] "Successful convergence in optimise"                                                                                      
## [4] "Minimiser achieved convergence after 99 quasi-Newton iterations using 119 objective function evaluations"                
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.80811e-05 f = 237.802"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.05483e-05 f = 238.776"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 2.57984e-09 f = 237.802"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [8] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [9] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [8] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [9] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [8] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [9] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 127 estimates, now have 42"                                                                              
## [2] "Cannot report the length-based selectivity values. This report (__lineFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"     
## [3] "Cannot report the length-based selectivity values. This report (__lineFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"
## [4] "Cannot report the length-based selectivity values. This report (__potFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [5] "Cannot report the length-based selectivity values. This report (__potFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [6] "Cannot report the length-based selectivity values. This report (__recFretained__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information" 
## [7] "Cannot report the length-based selectivity values. This report (__recFSel__) is being ignored. This can be done using the Casal2 R package. See the User Manual for more information"      
## [8] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"                                                                                                      
## [9] "estimated parameter 'age_length[asMm0].cv_last' was within 0.001 of lower bound 0.02"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Removals / Actual catches for line match: no"
## [1] "Discarded catches for line match: no"
## [1] "Removals / Actual catches for pot match: no"
## [1] "Discarded catches for pot match: no"
## [1] "Removals / Actual catches for rec match: no"
## [1] "Discarded catches for rec match: no"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.6876 0.9999"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.6894 0.9999"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.704682058267449 0.999819516983665"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.697745743037247 0.999863100354264"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.722472902754433 0.999845201096008"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.704683609734695 0.99981954195823"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.697745743037247 0.999863100354264"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.719263523071944 0.999846316745602"